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| author | Peter Amstutz | 2020-06-22 18:23:40 +0000 |
|---|---|---|
| committer | Peter Amstutz | 2020-06-22 18:25:45 +0000 |
| commit | 76883d02e6073f990ea980dad1f8cf21121255ff (patch) | |
| tree | 0fe93dadf69cb5c0c09ff9b98fe18e5baacdd6c4 /bh20seqanalyzer | |
| parent | fcf300d0df032f569f21b3ef75a78bb163f55da0 (diff) | |
| download | bh20-seq-resource-76883d02e6073f990ea980dad1f8cf21121255ff.tar.gz bh20-seq-resource-76883d02e6073f990ea980dad1f8cf21121255ff.tar.lz bh20-seq-resource-76883d02e6073f990ea980dad1f8cf21121255ff.zip | |
Adjust QC filter and relabel output sequence with sample_id
Diffstat (limited to 'bh20seqanalyzer')
| -rw-r--r-- | bh20seqanalyzer/main.py | 9 |
1 files changed, 6 insertions, 3 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py index 9164190..9a36cae 100644 --- a/bh20seqanalyzer/main.py +++ b/bh20seqanalyzer/main.py @@ -30,6 +30,7 @@ def validate_upload(api, collection, validated_project, try: metadata_content = ruamel.yaml.round_trip_load(col.open("metadata.yaml")) metadata_content["id"] = "http://arvados.org/keep:%s/metadata.yaml" % collection["portable_data_hash"] + sample_id = metadata_content["sample"]["sample_id"] add_lc_filename(metadata_content, metadata_content["id"]) valid = qc_metadata(metadata_content) and valid except Exception as e: @@ -51,7 +52,7 @@ def validate_upload(api, collection, validated_project, logging.info("Expected %s but magic says it should be %s", n, tgt) valid = False elif tgt in ("reads.fastq", "reads.fastq.gz", "reads_1.fastq", "reads_1.fastq.gz"): - start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid, n) + start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid, n, sample_id) return False if tgt is None: valid = False @@ -108,7 +109,8 @@ def run_workflow(api, parent_project, workflow_uuid, name, inputobj): def start_fastq_to_fasta(api, collection, analysis_project, fastq_workflow_uuid, - tgt): + tgt, + sample_id): params = { "metadata": { @@ -118,7 +120,8 @@ def start_fastq_to_fasta(api, collection, "ref_fasta": { "class": "File", "location": "keep:ffef6a3b77e5e04f8f62a7b6f67264d1+556/SARS-CoV2-NC_045512.2.fasta" - } + }, + "sample_id": sample_id } if tgt.startswith("reads.fastq"): |